Biosensors to detect small molecule ligands (e.g., metabolites) have applications in synthetic biology, medical diagnosis, environmental monitoring, bioremediation, and bioenergy. Protein-based biosensors are autonomous, self-powered, miniaturizable, and programmable macromolecules that function in both in vivo and ex vivo environments. Allosteric transcription factors (aTFs), a family of regulatory proteins found in all kingdoms of life, are widely used as biosensors in synthetic biology. Bacterial aTFs, such as LacI or TetR, are composed of allosterically-linked ligand- and DNA-binding domains. When an aTF binds to a ligand, the protein undergoes a conformational change, causing a change in affinity for DNA. In the case of transcription repressors, the loss of DNA affinity allows the RNA polymerase to access the promoter and initiate transcription of the downstream gene. Therefore, the concentration of small molecule can be measured in terms of a reporter gene expression in a dose-dependent manner.
Natural aTF-promoter pairs, however, may be unsuitable for a wide-range of biosensor applications. What is needed are methods of designing synthetic promoters for aTFs that can provide desired induction properties for aTF-based biosensors.